Ninja Assassin
by DaProphet0fPein
Summary: Ninja's were myths, legends of the past, Until Naruto came into the picture. The shinobi trained at a young age to be a assassin come across one of the most annoying assignments yet going undercover, will the blonde shinobi be able to compartmentalize what he were feeling towards Skye or will the shinobi betray everything he was taught since he was a child. OOC Naruto AU


**Hello folks this is a Alternate Universe and Naruto will be ooc to fit the premises of the story due to his background, He'll be a cold individual at times and a little apathetic, this little idea came to me in the midst of watching the film Ninja Assassin so it will be pertaining some elements from that with a twist so without further ado here you go. Also I don't own sht as usual everything to it respective owners.**

 _-1900s-_

 _A child with short blondish hair were seated among his brothers and sisters at a table, The hall were dimly lit and the entire long table had a dozen children on the left side and another dozen teens on the right. He sat quietly with the rest as a elder man walk around the room, even among the silence his casual footsteps didn't utter a peak._

" _Wherever you are, wherever you may go..You must never forget who you are." The Hokage voice echo through the room " How you came to be. You are shinobi, You are apart of me as I am apart of you. My instruments and my tools, this is the truth of your lives and it will remain true even after your deaths. Now eat." The hokage left the hall and the children bow._

 _-Next day-_

 _The blond gaze at his down partner, The two were just in a spar and he triumph over the other boy in combat, his fist were holding the metal Katana in his grasp as the hokage stood beside him._

" _What is the lesson? Life is combat, You know this is true, abandon by your parents, without a home, without people to kill for you, You should have died but instead you fought. The reason why you are alive here today is because you fought and you have won, in combat you face your enemy, without doubt, without pity, to survive you must learn to fear nothing at all…"_

 _-present day-_

A blonde male with frost blue eyes stood on his hands hanging upright at the edge of the building 15 floor high from the streets below, his eyes were staring at the city below him and he started doing press ups, he leaned back and flip onto the rooftop. He move onto the mat and began his Kata, in his grasp he held a long silver adamantium Kunai attached to a link chain, on the end of the mat were his Katana and star shape shuriken which were also made from the rare metal substance, These were gifts entrusted to him by his former master. The blonde phone alerted him and he cease his movements and pull the cellular device from his pocket.

"Yes." He stated softly, while bending over and packing everything into his suitcases.

"Oliver Weaver has served his purpose...I want the Berlin district gone." The man spoke softly "Hail Hydra."

"It will be done." The blonde accepted the assignment before flipping the phone closed.

-Shield Berlin Minor Headquarters 2100 Hrs-

Oliver Weaver, A level 7 Intelligence agent that ran a shield headquarters in Berlin were pretty frantic, The staff were in complete disarray, for the last three days the safe houses in his command had been targeted and systematically destroyed, He sent tactical teams to reinforce the areas after the first two attacks but all it did was add to the body count after his third attempt he evacuated the safe houses and brought the personnel to the headquarters. He ask for reinforcements but it would take some time before the Main HQ can send someone to see what was going on.

The middle age man had the underground facility on complete lock down, Tactical teams were at every entrance and hidden exit. He were sweating to be honest, He knew exactly who were targeting him, He tried to make amends with the Hydra leaders but he didn't realize they were going to send that demon after him for failing the assignment and he couldn't go to Agent Hill or Director Fury for help they were under heavy surveillance by Hydra and they would kill him on sight if he revealed himself as a Hydra Operative.

The only thing he could do is rile his men and have them aware of the incoming threat, He had every light in the building on, it could be no shadows for the man to move through.

"Tactical Teams report." He ask as he sat quietly in his office. He waited patiently as the squads reported into him "Team 6 what's your status." He ask after the previous squads reported no activity. The agent waited but receive no response " Team 6 report." He demanded a second time and was again met with silence " Team 1 head to Team 6 location and find out why they aren't responding, it could be a faulty radio."

"Roger." The team leader responded.

Oliver began pacing back in forth getting a uneasy feeling in his gut, before the lights in the building cut and darkness overtook the entire base. The backup generators kick in and the emergency red lights flared to life "He's here." Just as the man spoke, the roars of gunfire echoed throughout the building. The scientist and other staff began panicking as more tactical teams with flashlight mounted helmets rush through the hall towards the commotion.

Oliver swallow as the chaos and fighting gradually made it way to the main hub, He fell back into his chair as the screams of his people resounded through the area below, where his office overlooked the main square, The gun fire slowly died down to nothing but silence.

He grab a pistol from under his desk and aim it at the door, His other hand shaking as he reach over to his phone, He went to the contact list name and click the number that he knew could help him after a few seconds the phone click over and he could hear his superior breathing "Sir...Please call him off." He begs the man.

"You understood the consequences of failing Oliver." The man chuckles gently.

"It won't happen again...I promise Please." He pleaded for his life as the door slowly opens giving off a soft and low creak as it did so.

"It definitely won't." The man hung up the phone and Oliver fire into the darkness of the open door. He grab his flashlight and shine where he fire at and nothing were there in sight.

"What…" He mutter only for a figure to emerged from behind him, grabbing the man skull and cutting a deep gash into the man throat. Oliver grab at his throat and look in horror as his neck bled like a waterfall. The assassin walk around the man and his lifeless white eyes stare at him and Oliver felt he were in the presence of death and the blonde figure impale him directly in the chest where his heart sat, indefinitely ensuring his death.

The blonde walk over to the computer typing in the password and activating the hard drive wipe before completely destroying the device. He took the man phone tossing it into the metal waste bin and setting it ablaze with a match. He place his hand in the man blood before smearing it over the wall.

-A couple days later-

Sick..That is what Coulson and his team felt as they overrode the Lock down Protocols on the Berlin Headquarters. When the large doors open they were immediately slap with the stench of blood and death. A dead body fell back as if it were leaning against the blast doors out into the open. Coulson knew something were wrong the minute he landed in Berlin S.H.I.E.L.D tactical teams were there in force waiting for him, VIctoria Hand stated she lost contact with the Agent in charge there,a operative name Oliver weaver and now he understood why so many Agents and Specialist were sent here because the very walls and floor were soak with blood, body parts were everywhere the sight sicken him to his core.

"FitzSimmons." He turn to his scientist as tactical teams filed in first follow by the department field scientist following behind them "I think it may be best if you two stay out here.." Grant Ward and Skye look at the man in surprise, He never told them to wait outside before "Skye it may be best if you did as well...I don't think this something you three will want to see." Simmons look at the body parts already understanding from a mere glance at the entrance that it could be pretty bad in there.

The two scientist look at each other having a internal debate before nodding in agreement "We'll stay out here." Simmons spoke for them " Have the scientist transfer all the data they find to us."

Coulson nods to them and began walking forward with Grant only for Skye to grasp his shoulder "Be careful AC...Ward." She spoke softly gaining small smiles from the men.

* * *

Coulson and Ward look at the remains of their fellow agent, He reached over and silently close the man eyelids.

"It seems our suspect had destroyed the computer and Agent Weaver Phone." Ward stated as he look through the junk the man had on the desk while Coulson were staring at the wall " He was covering something, I suspect Agent weaver were in contact with someone and whoever it was is covering their tracks."

"Look at this." Coulson motions Ward over and the man finally seen what held his superior attention, a red splattered Kanji were painted on the wall.

The level 7 specialist raise a brow " What does it say?" He question Coulson.

The man stare morbidly "Death." Coulson side glance at the words " It means Agent Weaver were involved in something this is a calling card, it's not a simple attack it's a assassination. Tear this place apart, grab the hard drive and see if anything comes to light." Agent Coulson snap a picture of the mark.

X

Coulson ran the mark through the shield database that were connected to the different Organizations in the world from CIA to the KGB, and the Kanji in blood mark were painted in some pretty high profile assassinations all over the world but no solid connections on who could have done it, the only thing that the targets had in common were the carnage involved. He were so perplexed that he sent the image to one of his friends who were supposed to believe he were dead but desperate times call for desperate measures.

"Natasha." He greet the woman who had a gentle smile on her face.

The woman smile faded as she brought up the topic and reason why she were calling him " I heard about what happened in Berlin..but I do have some information on what you sent me." A beep drew his attention to the side of the screen and a black and white photo view itself on the screen "That mark is the calling of this Assassin, His name is Naruto Uzumaki, You won't find any information on him. He's not in any databases from any of the Organizations or from any country. He's a ghost." She remark as the man try to run the assassin name through the database."

He raised a brow "Then how do you know him?"

Natasha bit the bottom of her lip in thought wondering how much she should reveal " As you are aware of my former affiliation with the red room, We had a Rival Organization who went by the name as Kage which mean shadow in Japanese, This organization had 5 clan which is each lead by their own leader which is a Kage. The leader who led this man is called the Hokage. When I was training with the red room we were constantly warn about the Kage to be as cautious as possible with any wet work assignments because we don't know if that organization were hired as well and as you can see they don't really care about leaving bodies but the reason I know so much about this man in particular is because I had a few run ins with him. He's cold, Apathetic but unlike some of them can be quite reasonable, He will avoid bodies if possible, when he's not working he can be quite likeable." The woman told him all she know of the individual " Actually it's a restaurant in Japan that he frequents often...Just be careful though Coulson this man is dangerous and if the Organization feels like you are meddling in their affairs they would attempt to get rid of you."

"Noted." Coulson told his farewells to the super spy and ended the video call. He sigh " Starting a war with a Assassin organization wasn't on his to do list but he had to bring this Naruto Uzumaki in to find out his motives and who hired him." A beep sounded drawing his attention once again and a address appear on his screen." Thank you Natasha."

* * *

Naruto sat at his table, he were dress in black fitted jeans and a dark blue T shirt. The shinobi suitcase were place beside him on the floor as he slowly sucked in the ramen that he had recently order. He had several empty bowls on the table and were looking to make the next one his 8th. The restaurant weren't to busy tonight so he had all the time to enjoy his favorite food before someone called him with another assignment. He sigh in annoyance at the fact that he were contracted to Hydra for the time being. Neo Nazis weren't at the top of his favorite list definitely when they were trying to rule the world but then again eventually someone with a higher amount of money would outbid them and hire his clan to start assassinating them thus his contract would end soon. The clan ran on money, Blood money but money nonetheless. "why couldn't Sasuke-teme be stuck with Hydra Contracts."

The bell on the door chime and he sigh in annoyance yet again at letting his guard drop, He knew assassinating the shield/Hydra operative member would bring him heat from the Organization and it seems like Nat had dimed him out because only she knew where this place were. He cautiously counted out the tactical team they had sent in, he bent down opening his suitcase to reveal his favorite weapon, The chain link Kunai glinted in light but he didn't pull it from it's resting position. He could kill them all now but were actually curious at why they aren't firing at him, You know that's how ambushes usually work catch the enemy unaware and attempt to kill him.

A man in smartly dress suit walked in casually while flashing him a badge which made Naruto scoff, like that actually meant anything to him " Naruto Uzumaki I'm Agent Coulson and would like to have a word with you."

Naruto lean back in amusement 'This is definitely a different approach.' He gesture to the chair across from him and the man took a seat "Lets chat." The blonde stated while crossing his fingers " And Forewarning if they even so much as begin squeezing the trigger...Your remains will decorate this restaurant." The shinobi eyes frosted over.

* * *

 **What is everyone thoughts? Also two explain a few things the Village Kages are the clan leaders in this AU it won't be large villages as we are use to in the anime and they aren't all friendly with each other as well but they handle their affairs privately if someone were to get involved with those affairs it won't end nicely for them.**


End file.
